The SPEAR3 control system nominally operates with the EPICS toolbox on top of VMS hardware. The simultaneous use of Matlab Middlelayer (MML) and Accelerator Toolbox (AT) allow for parallel, high-level machine control and accelerator physics applications that communicate with the control system via EPICS Channel Access (LabCA). While the majority of the MML and AT software is machine independent, site-specific high-level applications are also required to control the accelerator. This paper describes several such high-level application programs that have been developed for control and diagnostics at SPEAR3. Examples include a timedependent waveform display gui, beam steering applications, transport line optics correction, SR beam diagnostics and add-ons to the main MML routines.